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Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin

Nature Structural & Molecular Biology volume 18, pages 777–782 (2011)Cite this article

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Abstract

Accurate read-out of chromatin modifications is essential for eukaryotic life. Mutations in the gene encoding X-linked ATRX protein cause a mental-retardation syndrome, whereas wild-type ATRX protein targets pericentric and telomeric heterochromatin for deposition of the histone variant H3.3 by means of a largely unknown mechanism. Here we show that the ADD domain of ATRX, in which most syndrome-causing mutations occur, engages the N-terminal tail of histone H3 through two rigidly oriented binding pockets, one for unmodified Lys4 and the other for di- or trimethylated Lys9. In vivo experiments show this combinatorial readout is required for ATRX localization, with recruitment enhanced by a third interaction through heterochromatin protein-1 (HP1) that also recognizes trimethylated Lys9. The cooperation of ATRX ADD domain and HP1 in chromatin recruitment results in a tripartite interaction that may span neighboring nucleosomes and illustrates how the 'histone-code' is interpreted by a combination of multivalent effector-chromatin interactions.

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Figure 1: The ADD domain of ATRX is required for localization in vivo.
Figure 2: Recognition of an N-terminal H3 tail by the ADD domain of ATRX.
Figure 3: Structure-guided mutations reveal tripartite chromatin interaction of ATRX in vivo.
Figure 4: ADD K9me3 recognition provides mechanistic evidence for HP1 independent recruitment of ATRX in mitosis.

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Change history

  • 19 June 2011

    In the version of this article initially published online, the Kd for the binding of the triply modified H3 peptide to the ATRX ADD domain was reported incorrectly in the text. The correct value is 0.59 µM. Additionally, the residues in insets A and B of Figure 2g were incorrectly labeled. The correct residue labels are Ser206 in inset A and Asp207 in inset B. These errors have been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

We thank A. Peters (Friedrich Miescher Institute Biomedical Research) and T. Jenuwein (Max Planck Institute for Immunobiology) for kindly providing the Suv39H1 and Suv39H2 double-knockout mouse embryonic fibroblasts, C. Johnson for help with the ITC experiments, M. Garcia-Alai for HP1 protein and M. Babu for helpful discussions. We thank the Medical Research Council (grants MRC_U.1051.04.017(78934) to D.N., MRC_U.1051.04.019(78936) to D.R. and MRC_U.1379.00.008(61147) to R.J.G. and D.H.) and the National Institute of Health Biomedical Research Centers Programme for funding. S.E. was supported by a Boehringer Ingelheim Fonds PhD Fellowship.

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Author notes

  1. Sebastian Eustermann and Ji-Chun Yang: These authors contributed equally to this work.

Authors and Affiliations

  1. Medical Research Council Laboratory of Molecular Biology, Cambridge, UK

    Sebastian Eustermann, Ji-Chun Yang, Lynda M Chapman, Daniela Rhodes & David Neuhaus

  2. Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK.,

    Martin J Law, Rachel Amos, Clare Jelinska, David Garrick, David Clynes, Richard J Gibbons & Douglas R Higgs

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Contributions

S.E. and J.-C.Y. carried out NMR experiments and structure determination. S.E., J.-C.Y. and D.N. analyzed the structures. S.E. and L.M.C. prepared protein and complex samples. S.E. carried out in vitro binding experiments. M.J.L., R.A., D.C. and D.G. carried out in vivo imaging experiments. S.E. and C.J. carried out in vitro experiments with mutants. S.E., D.R., D.N., R.J.G. and D.R.H. designed the experiments and wrote the manuscript.

Corresponding authors

Correspondence to Douglas R Higgs or David Neuhaus.

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Supplementary Figures 1–8, Supplementary Table 1 and Supplementary Methods (PDF 4631 kb)

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Eustermann, S., Yang, JC., Law, M. et al. Combinatorial readout of histone H3 modifications specifies localization of ATRX to heterochromatin. Nat Struct Mol Biol 18, 777–782 (2011). https://doi.org/10.1038/nsmb.2070

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